Summary
Cheminformatics
This metapackage will install cheminformatics packages
useful for chemists.
Description
For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:
If you discover a project which looks like a good candidate for DebiChem
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the DebiChem mailing list
Links to other tasks
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DebiChem Cheminformatics packages
Official Debian packages with high relevance
libcdk-java
Chemistry Development Kit (CDK) Java libraries
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Versions of package libcdk-java |
Release | Version | Architectures |
trixie | 2.9-1 | all |
bookworm | 2.8-2 | all |
bullseye | 2.3.134.g1bb9a64587-2 | all |
stretch | 1.2.10-6 | all |
jessie | 1.2.10-6 | all |
sid | 2.9-1 | all |
buster | 1.2.10-7 | all |
Debtags of package libcdk-java: |
devel | lang:java, library |
field | chemistry |
role | devel-lib |
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License: DFSG free
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The CDK is a library of Java classes used in computational and
information chemistry and in bioinformatics. It includes renderers,
file IO, SMILES generation/parsing, maximal common substructure
algorithms, fingerprinting and much, much more.
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libchemicaltagger-java
tool for semantic text-mining in chemistry
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Versions of package libchemicaltagger-java |
Release | Version | Architectures |
sid | 1.6.2-4 | all |
trixie | 1.6.2-4 | all |
bookworm | 1.6.2-2 | all |
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License: DFSG free
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ChemicalTagger parser is a medium-depth, phrase-based semantic NLP tool for the
language of chemical experiments. Tagging is based on a modular architecture
and uses a combination of OSCAR, domain-specific regex and English taggers to
identify parts-of-speech. The ANTLR grammar is used to structure this into
tree-based phrases.
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libinchi-bin
International Chemical Identifier (InChI) algorithm (executable)
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Versions of package libinchi-bin |
Release | Version | Architectures |
trixie | 1.07.1+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.03+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.07.1+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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The International Chemical Identifier (InChI) is an Open Source chemical
structure representation algorithm.
InChIs are text strings comprising different layers and sublayers of
information separated by slashes (/). Each InChI strings starts with the
InChI version number followed by the main layer. This main layer contains
sublayers for chemical formula, atom connections and hydrogen atoms.
Depending on the structure of the molecule the main layer may be followed
by additional layers e. g. for charge, stereochemical and/or isotop
information.
This package contains the executable, inchi_main.
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libjni-inchi-java
Java Native Interface wrapper for InChI
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Versions of package libjni-inchi-java |
Release | Version | Architectures |
sid | 0.8+dfsg-8 | all |
bullseye | 0.8+dfsg-6 | all |
trixie | 0.8+dfsg-8 | all |
bookworm | 0.8+dfsg-7 | all |
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License: DFSG free
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JNI-InChI provides JNI (Java Native Interface) wrappers for the InChI
(International Chemical Identifier) C library distributed by IUPAC.
All of the features from the InChI libarary are supported:
- Standard and Non-Standard InChI generation from structures with 3D, 2D,
or no coordinates
- Structure generation (without coordinates) from InChI
- InChIKey generation
- Check InChI / InChIKey
- InChI-to-InChI conversion
- AuxInfo to InChI input
- Access to the full range of options supported by InChI
- Full support for InChI's handling of stereochemistry
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libopenchemlib-java
framework providing cheminformatics core functionality
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Versions of package libopenchemlib-java |
Release | Version | Architectures |
bullseye | 2021.2.0+dfsg-1 | all |
bookworm | 2023.1.1+dfsg-1 | all |
sid | 2023.1.1+dfsg-1 | all |
trixie | 2023.1.1+dfsg-1 | all |
upstream | 2024.11.1 |
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License: DFSG free
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OpenChemLib is Java based framework providing cheminformatics core
functionality and user interface components. Its main focus is on organics
chemistry and small molecules. It is built around a StereoMolecule class,
which represents a molecule using atom and bond tables, provides atom
neighbours, ring and aromaticity information, and supports MDL's concept of
enhanced stereo representation. Additional classes provide, 2D-depiction,
descriptor calculation, molecular similarity and substructure search,
reaction search, property prediction, conformer generation, support for
molfile and SMILES formats, energy minimization, ligand-protein
interactions, and more. OpenChemLib's idcode represents molecules,
fragments or reactions as canonical, very compact string that includes
stereo and query features.
Different to other cheminformatics frameworks, OpenChemLib also provides
user interface components that allow one to easily embed chemical functionality
into Java applications, e.g. to display or edit chemical structures or
reactions.
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libopsin-java
Chemical name to structure converter
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Versions of package libopsin-java |
Release | Version | Architectures |
trixie | 2.8.0-1 | all |
jessie | 1.5.0-1 | all |
stretch | 1.5.0-1 | all |
buster | 2.3.1-1 | all |
bullseye | 2.5.0-1 | all |
bookworm | 2.7.0-2 | all |
sid | 2.8.0-1 | all |
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License: DFSG free
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OPSIN (Open Parser for Systematic IUPAC Nomenclature) converts IUPAC compound
names to semantic chemical information and outputs a structure either as
CML (Chemical Markup Language), SMILES, or InChI.
This package contains the Java library.
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liboscar4-java
automated annotation of chemistry in scientific articles
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Versions of package liboscar4-java |
Release | Version | Architectures |
trixie | 5.2.0+dfsg-2 | all |
bookworm | 5.2.0+dfsg-2 | all |
sid | 5.2.0+dfsg-2 | all |
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License: DFSG free
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OSCAR (Open Source Chemistry Analysis Routines) is an open source extensible
system for the automated annotation of chemistry in scientific articles. It can
be used to identify chemical names, reaction names, ontology terms, enzymes and
chemical prefixes and adjectives, and chemical data such as state, yield, IR,
NMR and mass spectra and elemental analyses. In addition, where possible, any
chemical names detected will be annotated with structures derived either by
lookup, or name-to-structure parsing using OPSIN or with identifiers from the
ChEBI (Chemical Entities of Biological Interest) ontology.
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openbabel
Chemical toolbox utilities (cli)
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Versions of package openbabel |
Release | Version | Architectures |
stretch | 2.3.2+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.1+dfsg-3 | amd64,arm64,armhf,i386 |
bullseye | 3.1.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.1.1+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.3.2+dfsg-2 | amd64,armel,armhf,i386 |
Debtags of package openbabel: |
field | chemistry |
interface | commandline |
role | program |
scope | utility |
use | converting |
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License: DFSG free
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Open Babel is a chemical toolbox designed to speak the many languages of
chemical data. It allows one to search, convert, analyze, or store data from
molecular modeling, chemistry, solid-state materials, biochemistry, or related
areas. Features include:
- Hydrogen addition and deletion
- Support for Molecular Mechanics
- Support for SMARTS molecular matching syntax
- Automatic feature perception (rings, bonds, hybridization, aromaticity)
- Flexible atom typer and perception of multiple bonds from atomic coordinates
- Gasteiger-Marsili partial charge calculation
File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL
Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.
This package includes the following utilities:
- obabel: Convert between various chemical file formats
- obenergy: Calculate the energy for a molecule
- obminimize: Optimize the geometry, minimize the energy for a molecule
- obgrep: Molecular search program using SMARTS pattern
- obgen: Generate 3D coordinates for a molecule
- obprop: Print standard molecular properties
- obfit: Superimpose two molecules based on a pattern
- obrotamer: Generate conformer/rotamer coordinates
- obconformer: Generate low-energy conformers
- obchiral: Print molecular chirality information
- obrotate: Rotate dihedral angle of molecules in batch mode
- obprobe: Create electrostatic probe grid
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osra
optical structure recognition
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Versions of package osra |
Release | Version | Architectures |
bookworm | 2.1.3-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.1.3-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.1.3-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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OSRA is a utility designed to convert graphical representations of
chemical structures, as they appear in journal articles, patent documents,
textbooks, trade magazines etc., into SMILES (Simplified Molecular
Input Line Entry Specification) - a computer recognizable molecular structure
format. OSRA can read a document in any of the over 90 graphical formats
parseable by ImageMagick - including GIF, JPEG, PNG, TIFF, PDF, PS etc., and
generate the SMILES representation of the molecular structure images
encountered within that document.
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python3-indigo
Organic Chemistry Toolkit (Python module)
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Versions of package python3-indigo |
Release | Version | Architectures |
bullseye | 1.2.3-3.1 | all |
sid | 1.2.3-3.1 | all |
trixie | 1.2.3-3.1 | all |
bookworm | 1.2.3-3.1 | all |
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License: DFSG free
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Indigo is a C++ based organic chemistry and cheminformatics software
environment. Features Include:
- Molecule and reaction rendering including SVG support
- Automatic layout for SMILES-represented molecules and reactions
- Canonical (isomeric) SMILES computation
- Exact matching, substructure matching, SMARTS matching
- Matching of tautomers and resonance structures
- Molecule fingerprinting, molecule similarity computation
- Fast enumeration of SSSR rings, subtrees, and edge sugraphs
- Molecular weight, molecular formula computation
- R-Group deconvolution and scaffold detection
- Computation of the exact maximum common substructure for an
arbitrary amount of input structures
- Combinatorial chemistry
- Plugin support in the API
File formats Indigo support include MDL Mol, SDF, RDF, CML, SMILES and
SMARTS.
This package contains the Python modules.
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python3-openbabel
Chemical toolbox library (Python bindings)
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Versions of package python3-openbabel |
Release | Version | Architectures |
bullseye | 3.1.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.1.1+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.1.1+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Open Babel is a chemical toolbox designed to speak the many languages of
chemical data. It allows one to search, convert, analyze, or store data from
molecular modeling, chemistry, solid-state materials, biochemistry, or related
areas. Features include:
- Hydrogen addition and deletion
- Support for Molecular Mechanics
- Support for SMARTS molecular matching syntax
- Automatic feature perception (rings, bonds, hybridization, aromaticity)
- Flexible atom typer and perception of multiple bonds from atomic coordinates
- Gasteiger-Marsili partial charge calculation
File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL
Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.
This package contains the Python binding.
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python3-rdkit
Collection of cheminformatics and machine-learning software
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Versions of package python3-rdkit |
Release | Version | Architectures |
bookworm | 202209.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 202009.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 202309.3-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 202409.2 |
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License: DFSG free
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RDKit is a Python/C++ based cheminformatics and machine-learning software
environment. Features Include:
- Chemical reaction handling and transforms
- Substructure searching with SMARTS
- Canonical SMILES
- Molecule-molecule alignment
- Large number of molecular descriptors, including topological,
compositional, EState, SlogP/SMR, VSA and Feature-map vectors
- Fragmentation using RECAP rules
- 2D coordinate generation and depiction, including constrained depiction
- 3D coordinate generation using geometry embedding
- UFF and MMFF94 forcefields
- Chirality support, including calculation of (R/S) stereochemistry codes
- 2D pharmacophore searching
- Fingerprinting, including Daylight-like, atom pairs, topological
torsions, Morgan algorithm and MACCS keys
- Calculation of shape similarity
- Multi-molecule maximum common substructure
- Machine-learning via clustering and information theory algorithms
- Gasteiger-Marsili partial charge calculation
File formats RDKit supports include MDL Mol, PDB, SDF, TDT, SMILES and RDKit
binary format.
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smiles-scripts
command line tools to handle SMILES descriptors
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Versions of package smiles-scripts |
Release | Version | Architectures |
bookworm | 0.2.0+dfsg1-4 | all |
sid | 0.2.0+dfsg1-6 | all |
trixie | 0.2.0+dfsg1-6 | all |
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License: DFSG free
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Package provides command line tools to work with Simplified Molecular-Input
Line-Entry System (SMILES) descriptors. Package contains command line interface
scripts for Chemistry Development Kit (CDK), as well as a syntax checker for
SMILES.
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